improved readme, added assembly to sample

README.md

@@ -3,7 +3,7 @@
 Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
 defining the electron microscopy related fields required by the OSCEM standard.
 
-Core idea is a modular system that allows for the combination of several sample and method parts to describe a variety of electron microscopy use cases. All original schemas can be found as .yaml under src/oscem_schemas/schema. Files named oscem_* refer to set collection for i.e. single particle analysis whereas schemas with more precise names such as "instrument" refers to a specific subschema detailing in this case instrument variables. Using the linkml generator functions the overall schemas can be exported to a variety of other formats such as json-schema, jsonld, owl and rdfa. We recommend using json-schema versions for validating metadata.
+Core idea is a modular system that allows for the combination of several sample and method parts to describe a variety of electron microscopy use cases. All original schemas can be found as .yaml under src/oscem_schemas/schema. Files named oscem_* refer to set collections of subschemas, e.g. single particle analysis. Schemas with more precise names such as "instrument" refer to a specific subschema that can be modularily imported into oscem_* schemas. Using the linkml generator functions the overall schemas can be exported to a variety of other formats such as json-schema, jsonld, OWL and RDF. We recommend using json-schema versions for validating metadata.
 
 Current versions are a work in progress, details might change.
 

src/data/examples/EMDataset-001.yaml

@@ -51,6 +51,7 @@ authors:
 sample:
   overall_molecule:
     molecular_type: Complex
+    assembly: PARTICLE
     name_sample: Ribosome
     source: yeast
     molecular_weight:

src/oscem_schemas/schema/organizational.yaml

@@ -57,7 +57,7 @@ classes:
         required: true
       type_org:
         required: true
-      name_org:
+      name_org: 
         required: true
 
   Grant:

src/oscem_schemas/schema/sample.yaml

@@ -24,6 +24,15 @@ enums:
         description: Chimera
       None of these:
         description: None of these
+  AssemblyEnum:
+    title: AssemblyEnum
+    permissible_values:
+      FILAMENT:
+        description: If your protein (complex) of interest is forming filaments
+      HELICAL ARRAY: 
+        description: If your protein (complex) of interest is forming helical arrays (i.e. tubes)
+      PARTICLE:
+        description: If your protein (complex) of interest forms individual particles on the grid with no orderd interactions
 
 classes:
   OverallMolecule:
@@ -34,6 +43,7 @@ classes:
       - name_sample
       - source
       - molecular_weight
+      - assembly
     slot_usage:
       molecular_type:
         required: true
@@ -45,6 +55,8 @@ classes:
         required: true
       molecular_weight:
         # alias: Molecular_weight
+      assembly:
+        required: true
 
   Molecule:
     title: Molecule
@@ -376,3 +388,6 @@ slots:
     title: Grid
     description: Description of the grid used
     range: Grid
+  assembly:
+    description: What type of higher order structure your sample forms - if any.
+    range: AssemblyEnum